The guide-slider joint of the transmission mechanism with a long stroke has a great effect on the dynamic characteristic of the structure. Aiming at the dynamic modeling on the joint part of the LM linear rolling guide in some large laser facility, the finite element (FE) model of the transmission mechanism with a long stroke is established based on the thin layer element and spring element. The modulus of the thin element and the stiffness of the spring element are identified by the model updating method and the modal experimental results. After the model update, the maximal error of the first three modal frequencies between simulation and experiment is 2.29%, and the maximal error of the point’s displacement response between simulation and experiment is 7.61% under the ambient vibration. The results of simulation and experiment are consistent, which shows that the model is effective and reasonable. The study provides a theoretical basis for the high confidence dynamic modeling on other structure with such a the joint.